5-azacytidine (5AC) is a highly active agent for the treatment of myelodysplastic syndromes (MDS, response rate 50 - 60%). 5AC retards the progression of MDS to acute myeloid leukemia (AML); however, the median duration of response to 5AC is less than 18 months. The mechanism of clinical activity of this agent may derive from its potent inhibition of DNA methyltransferase (DNMT). Exposure of cells to DNMT inhibitors (DNMTi) leads to reversal of methylation of CpG islands in the promoter regions of transcriptionally silenced genes and can lead to re-expression of such genes. More robust re-expression of methylated genes may be accomplished by the combination of DNMTi with histone deacetylase inhibitors (HDACi). MS-275, an orally bioavailable HDACi, induces histone hyperacetylation sustained up to three weeks following drug administration. This new reagent provides an outstanding opportunity to test the concept of combined DNMTi and HDACi in myeloid malignancies. The clinical trial forming the basis of this Quick Trials application will identify an optimal doses and schedule of subcutaneous 5AC and oral MS-275. The application requests funds to perform laboratory studies aimed at testing the hypothesis that combinations of 5AC with MS-275 lead to re-expression of silenced genes, and that such re-expression is associated with clinical response. Patients will be treated with a variety of doses and schedules of 5AC and MS-275 (administered on days 3 and 10 of each treatment cycle). The data will be evaluated to identify a "clinically optimal dose" which maximizes histone hyperacetylation and gene re-expression with minimal toxicity. Quantitative rt-PCR will be used to monitor the expression of two genes which are most commonly silenced through methylation in AML and MDS: p15INK4B and Ecadherin (E-CAD). Expression microarrays will be performed on isolated CD34+ cells to identify genes and molecular pathways whose expression is up- or down-regulated in response to this combination of drugs which may be related to response (whether methylated or not). Patient samples will be studied for changes in promoter methylation using realtime PCR modifications of methylation-specific PCR, and bisulfite sequencing of PCR products. Chromatin immunoprecipitation assays will identify changes in acetylation of histones associated with promoter sequences in p15 and p21WAF1/CIP1. Finally, Western analysis will be used to seek changes in phosphorylated H2AX, a marker of DNA damage, to evaluate the extent to which these drugs induce DNA strand breaks. Promising preliminary data from this trial will be followed directly by a randomized Phase II trial of 5AC plus MS-275 versus the same schedule of 5AC alone to investigate the clinical importance of the addition of the HDAC inhibitor.